How to Start A Behavioral Health Clinic in Mississippi (2026): License, Medicaid Enrollment & Rates

Licensing

Mississippi behavioral health clinic license

Mississippi requires a DMH Agency Provider Certification (Certificate of Operation) plus certification of each physical service location from Mississippi Department of Mental Health — Division of Certification to operate a behavioral health clinic. Fee: DMH notifies the applicant in writing of the application fee after the initial application is submitted; it must be received within 30 business days or the application is voided. DMH Operational Standards also list a $300 initial certification fee and up to $350 per DMH employee per day for initial certification visits for some certificate types (DMH/D, DMH/C and DMH/G holders are exempt).

License required: Yes
License: DMH Agency Provider Certification (Certificate of Operation) plus certification of each physical service location
Issuing agency: Mississippi Department of Mental Health — Division of Certification
Fee: DMH notifies the applicant in writing of the application fee after the initial application is submitted; it must be received within 30 business days or the application is voided. DMH Operational Standards also list a $300 initial certification fee and up to $350 per DMH employee per day for initial certification visits for some certificate types (DMH/D, DMH/C and DMH/G holders are exempt).
Accreditation: Not stated as required. DMH runs a Certified Community Behavioral Health Clinics program, and Mississippi is in the 2026 cohort of the federal CCBHC Medicaid demonstration.
Survey and inspection: DMH conducts initial certification visits and ongoing certification reviews.
Regulation: 24 Miss. Admin. Code Part 2 (DMH Operational Standards), incl. Rule 2-2.8 (application process for new/interested agency providers)

How to apply

Steps to get licensed in Mississippi

In order, as the licensing agency describes the process.

Review the current DMH Operational Standards (effective 2024-11-01)
Complete the DMH Interested Agency Provider Orientation in the online portal, including attesting that you reviewed the standards
Submit the complete Interested Agency Provider application packet and supporting documents through the portal
Pay the fee DMH assigns in writing within 30 business days
Receive DMH Agency Provider Certification for the agency and its planned services
Apply separately for DMH certification of each physical service location

Documents

What you need to submit

7 documents listed by the licensing agency.

Document
DMH Interested Agency Provider Application
Evidence of incorporation from the Mississippi Secretary of State (as applicable)
Governing and professional authority structure with signed governing authority and executive director assurances

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Medicaid

Enrolling as a Mississippi Medicaid provider

Program: Mississippi Medicaid (Mississippi Division of Medicaid, DOM)
Enrollment portal: Medicaid Enterprise System Assistance (MESA) Provider Portal
Fiscal agent: Gainwell Technologies (DOM fiscal agent; sends recredentialing notices and does revalidation site visits)
Application fee: DOM charges institutional provider taxonomies on its list (e.g., home health, hospice, ASCs, ESRD, FQHCs, mental health centers, rehab facilities) $750 for 2026. The fee applies at initial enrollment, reactivation, revalidation or re-enrollment, ownership changes and new practice locations, and is paid by check to the Division of Medicaid (marked with the application tracking number) and mailed to Gainwell. Providers that already paid Medicare or another state are exempt. Federal rule (42 CFR 455.460): the state must collect the CMS application fee from institutional providers that are newly enrolling or re-enrolling; individual physicians and non-physician practitioners are exempt, as are providers already enrolled in (or that already paid the fee to) Medicare or another state's Medicaid/CHIP. CMS set the fee at $750 for calendar year 2026.
Fingerprinting: Revalidating providers may have to submit fingerprints as part of screening. Federal rule (42 CFR 455.434, 455.450(c)): providers the state places in the 'high' categorical risk level, and anyone owning 5% or more of such a provider, must submit fingerprints for a criminal background check.
Site visit: Revalidating providers may need a site visit, done by Medicaid's fiscal agent. Federal rule (42 CFR 455.432, 455.450(b)-(c)): the state must do site visits before and after enrollment for providers in the 'moderate' or 'high' risk levels, and any enrolled provider must allow unannounced on-site inspections.
Revalidation: DOM restarted revalidation on October 1, 2023, mailing notices to providers enrolled five years or more; revalidation is done in the MESA Provider Portal. DOM published a Medicaid Provider Revalidation Roadmap in August 2026. Federal rule (42 CFR 455.414): every enrolled provider must be revalidated at least once every 5 years.

Full Mississippi Medicaid enrollment guide →

Certificate of need

Does Mississippi require a certificate of need?

CON program: Yes
Program: Certificate of Need
Agency: Mississippi State Department of Health, Office of Health Policy and Planning (Health Planning & Resource Development)
Services covered: nursing home care services (skilled nursing and ICF)
ICF/IID and nursing care for persons with developmental disabilities
pediatric skilled nursing facilities
acute psychiatric, chemical dependency and psychiatric residential treatment beds
obstetrical and neonatal special care services
comprehensive medical rehabilitation
ambulatory surgery
home health agencies / home health services
end stage renal disease facilities
general acute care hospitals and beds, swing beds, long-term care hospitals
MRI, PET, digital angiography, therapeutic radiation, stereotactic radiosurgery, cardiac catheterization, open-heart surgery
major medical equipment and capital expenditures above indexed thresholds; changes of ownership
Moratoria: Long-standing legislative moratoria (first imposed in 1990) bar new or expanded nursing home beds, ICF and ICF/IID beds, and new home health agencies. Effective April 17, 2026, the Legislature re-enacted and reaffirmed the nursing facility / ICF / ICF-IID moratorium (HB 1622, 2026 Regular Session, §2) and the home health agency moratorium.

Mississippi certificate of need details →

Labor

Mississippi wage floor

State minimum wage: $7.25 an hour
Effective: 2009-07-24
Scheduled increases: No scheduled change found in the official sources reviewed.
HCBS 80/20 rule: Federal baseline: 42 CFR 441.302(k) requires the state to show that each provider spends at least 80% of Medicaid payments for homemaker, home health aide and personal care services under 1915(c) waivers on direct care worker pay and benefits. Compliance starts 2030-07-09 (for managed care, the first rating period starting on or after that date); annual payment-adequacy reporting under 441.311(e) starts 2028-07-09. A state may set a lower share for state-defined small providers and exempt providers facing hardship, each only through a public notice-and-comment process. The eCFR text has not changed since 2024-07-09. No state-published 80/20 implementation step (small-provider criteria, hardship exemption or reporting guidance) was found for this state in the official sources reviewed.

Market

Mississippi market size

Counts from federal public files: NPPES (active organization NPIs), CMS Care Compare and CMS Medicaid enrollment.

Community/behavioral health agencies and mental health clinics — active organization NPIs (NPPES): 549 (as of Sep 13, 2026)
Total Medicaid and CHIP enrollment (latest reported month): 584,125 (as of Jun 1, 2026)

Rates

What Mississippi Medicaid pays

Behavioral health: published Mississippi fee-for-service rates, each linked to its source.

Service	Code	Mississippi rate	Per hour	Rank
Outpatient psychotherapy and diagnostic evaluationLicensed mental health clinician	90846	$93.38	—	7 of 28
Mental health assessment (non-physician)Physician or licensed psychologist	H0031	$110.70	—	17 of 27
Mental health service plan developmentLicensed mental health clinician	H0032	$21.37	—	12 of 18
Psychiatric residential treatment (daily)		$561.22	—	—

All Mississippi Behavioral health Medicaid rates, ranked →

Waivers

Mississippi HCBS waivers

Medicaid home and community-based services programs that may pay for this service.

Assisted Living Waiver (1915(c))
Elderly and Disabled (E&D) Waiver (1915(c))
IDD Community Support Program (CSP) (1915(i))
Intellectual Disabilities and Developmental Disabilities (ID/DD) Waiver (1915(c))
Independent Living Waiver (1915(c))
Traumatic Brain Injury and Spinal Cord Injury Waiver (1915(c))

Mississippi waivers and waiting lists →

FAQ

Frequently asked questions

Do you need a license to start a behavioral health clinic in Mississippi?

Mississippi requires a DMH Agency Provider Certification (Certificate of Operation) plus certification of each physical service location from Mississippi Department of Mental Health — Division of Certification to operate a behavioral health clinic. Fee: DMH notifies the applicant in writing of the application fee after the initial application is submitted; it must be received within 30 business days or the application is voided. DMH Operational Standards also list a $300 initial certification fee and up to $350 per DMH employee per day for initial certification visits for some certificate types (DMH/D, DMH/C and DMH/G holders are exempt).

How much does a behavioral health clinic license cost in Mississippi?

DMH notifies the applicant in writing of the application fee after the initial application is submitted; it must be received within 30 business days or the application is voided. DMH Operational Standards also list a $300 initial certification fee and up to $350 per DMH employee per day for initial certification visits for some certificate types (DMH/D, DMH/C and DMH/G holders are exempt).

Does Mississippi require a certificate of need for a behavioral health clinic?

Mississippi has a certificate of need program covering: nursing home care services (skilled nursing and ICF), ICF/IID and nursing care for persons with developmental disabilities, pediatric skilled nursing facilities, acute psychiatric, chemical dependency and psychiatric residential treatment beds, obstetrical and neonatal special care services, comprehensive medical rehabilitation, ambulatory surgery, home health agencies / home health services, end stage renal disease facilities, general acute care hospitals and beds, swing beds, long-term care hospitals, MRI, PET, digital angiography, therapeutic radiation, stereotactic radiosurgery, cardiac catheterization, open-heart surgery, major medical equipment and capital expenditures above indexed thresholds; changes of ownership. Check whether your service is on that list.

How do you become a Medicaid provider in Mississippi?

Enroll through Medicaid Enterprise System Assistance (MESA) Provider Portal (https://portal.ms-medicaid-mesa.com/), run by Gainwell Technologies (DOM fiscal agent; sends recredentialing notices and does revalidation site visits).

What does Mississippi Medicaid pay a behavioral health clinic?

Mississippi Medicaid pays $93.38 for outpatient psychotherapy and diagnostic evaluation, effective Jul 1, 2026, ranking 7 of 28 states.

How to start a behavioral health clinic in Mississippi